The abrupt decline in sardine catches in the Sea of Japan and the East China Sea (SJ-ECS) in 2014 and 2019 and the recovery in the following years call into question the current assumption that sardines in the SJ-ECS form a self-recruiting subpopulation. To test this hypothesis, we analysed otolith stable oxygen and carbon isotope profiles (δ18O, δ13C) of age-0 and age-1 sardines from 2010 and 2013–2015 year-classes captured in the SJ-ECS, as geographic markers for nursery areas. Age-0 sardines generally showed a significant ontogenetic decrease in otolith δ18O from larval to juvenile stages. However, the majority of age-1 captured in spring 2011, 2015 and 2016 showed non-decreasing otolith δ18O profiles, suggesting that the age-0 off the Japanese coast were not the main source of recruitment. Different migration groups were thus indicated: the “locals” growing up off the Japanese coast and the migrating “nonlocals”. The isotope profiles of the “nonlocals” overlapped with those of age-0 captured in the subarctic North Pacific, suggesting that they may be migrants from the Pacific, or perhaps an unobserved northward migration group in the SJ-ECS. Our results highlight the considerable uncertainty in the population structure assumed in current stock assessment models for Japanese sardine.